Table I. A summary of peptide mass fingerprinting and tandem MS data for the 41 proteins identified in complex I from P. pastoris.
| Subunit | Number of residues | Peptide mass fingerprinting |
Tandem MS |
||||
|---|---|---|---|---|---|---|---|
| Number of peptides1 | Sequence coverage | Score | Number of peptides | Sequence coverage | Score | ||
| 1. NUAM/75 kDa | 702 | 54 (98) | 77% | 298 | 22 | 52% | 1795 |
| 2. NUBM/51 kDa | 462 | 17 (11) | 47% | 175 | 14 | 37% | 767 |
| 3. NUCM/49 kDa | 451 | 20 (11) | 58% | 250 | 19 | 57% | 1328 |
| 4. NUGM/30 kDa | 251 | 18 (15) | 80% | 246 | 18 | 75% | 1213 |
| 5. NUHM/24 kDa | 215 | 9 (14) | 41% | 109 | 9 | 42% | 467 |
| 6. NUIM/TYKY2 | 222 | 11 (23) | 41% | 109 | 12 | 53% | 745 |
| 7. NUKM/PSST2 | 204 | 12 (8) | 45% | 132 | 6 | 32% | 495 |
| 8. NU1M/ND1 | 353 | 4 (28) | 7% | 17 | 2 | 8% | 86 |
| 9. NU2M/ND2 | 523 | 3 (24) | 6% | 18 | 2 | 5% | 132 |
| 10. NU3M/ND3 | 141 | 2 (0) | 17% | 43 | 2 | 17% | 83 |
| 11. NU4M/ND43 | 491 | 3 (24) | 7% | 15 | 1 | 5% | 48 |
| 12. NU5M/ND5 | 642 | 6 (15) | 10% | 35 | 6 | 10% | 265 |
| 13. NU6M/ND64 | 161 | – | – | – | – | – | – |
| 14. NULM/ND4L4 | 82 | – | – | – | – | – | – |
| 15. NUEM/39 kDa | 377 | 22 (16) | 71% | 291 | 18 | 62% | 1526 |
| 16. NESM/ESSS | 215 | 4 (15) | 27% | 23 | 8 | 48% | 870 |
| 17. NUJM/B14.7 | 215 | 12 (45) | 55% | 114 | 7 | 36% | 358 |
| 18. NUXM | 192 | 12 (13) | 65% | 178 | 10 | 63% | 560 |
| 19. NUPM/PGIV | 183 | 9 (8) | 57% | 107 | 8 | 46% | 878 |
| 20. NUZM | 181 | 19 (12) | 84% | 277 | 12 | 69% | 911 |
| 21. NUSM | 154 | 12 (17) | 76% | 173 | 7 | 61% | 521 |
| 22. NIMM/MWFE | 150 | 16 (14) | 62% | 196 | 10 | 52% | 593 |
| 23. NB6M/B16.6 | 146 | 10 (16) | 63% | 141 | 11 | 58% | 650 |
| 24. N7BM/B17.2 | 139 | 9 (16) | 53% | 147 | 6 | 45% | 513 |
| 25. NUYM/18 kDa | 139 | 9 (20) | 67% | 108 | 8 | 62% | 644 |
| 26. NIAM/ASHI | 132 | 7 (17) | 45% | 75 | 6 | 43% | 300 |
| 27. NUMM/13 kDa | 128 | 8 (22) | 71% | 111 | 9 | 66% | 519 |
| 28. NUFM/B13 | 126 | 6 (15) | 49% | 78 | 6 | 58% | 616 |
| 29. NB4M/B14 | 121 | 7 (21) | 61% | 106 | 6 | 56% | 431 |
| 30. NI2M/B22 | 110 | 11 (19) | 78% | 165 | 7 | 59% | 393 |
| 31. NIPM/15 kDa | 105 | 11 (17) | 75% | 145 | 8 | 63% | 506 |
| 32. ACPM1/SDAP15,6 | 92 | 3 | 27% | – | 3 | 27% | 332 |
| 33. NIDM/PDSW | 91 | 5 (24) | 59% | 84 | 4 | 48% | 273 |
| 34. NI8M/B8 | 89 | 6 (24) | 61% | 85 | 5 | 56% | 397 |
| 35. ACPM2/SDAP26,7 | 88 | 2 | 20% | – | 2 | 20% | 100 |
| 36. NB8M/B18 | 86 | 6 (18) | 65% | 67 | 6 | 58% | 334 |
| 37. NUTM5 | 85 | 2 | 28% | 20 | 3 | 27% | 58 |
| 38. NB5M/B15 | 80 | 8 (22) | 62% | 153 | 5 | 36% | 268 |
| 39. NI9M/B9 | 78 | 5 (17) | 43% | 64 | 3 | 26% | 336 |
| 40. NUUM | 73 | 3 (18) | 54% | 40 | 3 | 60% | 165 |
| 41. NB2M/B12 | 60 | 5 (17) | 31% | 68 | 3 | 45% | 147 |
The scores for peptide mass fingerprinting and tandem MS are Mascot scores, and the sum of the ions scores for matching peptides, respectively. The individual peptides and their scores for tandem MS, including error tolerant searches are presented in Table S1. Scores of 50 for peptide mass fingerprinting and 23 for tandem MS were required for p < 0.05% (for comparison against the P. pastoris database). Number of residues and sequence coverage are based on the mature sequences; the supernumerary subunits are listed in order of the sequence length.
- The number of peptides is given alongside the number of unmatched masses (in brackets).
- Mature protein sequence is not known, number of residues and sequence coverage are based on the complete sequence.
- See Supplementary Information for peptide mass fingerprints and tandem MS spectra.
- No peptides were identified.
- Only observed following protein separation by reverse phase HPLC.
- Peptide mass fingerprinting data alone were insufficient for protein identification.
- Length of mature protein inferred from homology with other species.